• S. FEBINA BERNICE SHARON Department of Food Science and Nutrition, Sarah Tucker College, Tirunelveli, Tamil Nadu


Objective: COVID-19 caused by novel SARS-coronavirus 2 belonging to family Coronaviridae, is a global public health emergency infecting many people all around the world, especially in India with more than 2,98,000 cases. Hence there is a need for a novel drug that counters SARS-CoV2 is the prime requirement at this time.

Methods: The present study aimed to assess bioactive compounds found in Azadirachta indica as a potential inhibitor of COVID-19 Mpr °(6Y2E, 6LU7, and 2GTB) by Autodock 4.2, with the Lamarckian Genetic Algorithm. COVID-19 Mpr ° was docked with thirteen bioactive compounds, and docking was analyzed by Autodock 4.2 and Pymol. Nelfinavir and Saquinavir were used as positive standards for comparison.

Results: Azadirachtanin, Azadirachtol, and Salannolide, were left out because of the violation of Lipinski’s rule. The binding energies obtained from the docking of 6Y2E with a native ligand, Azadiradione, Beta-sitosterol, Epiazadiradione, Epoxyazadiradione, Kaempferol, Meldenin, Myricetin, Nimbaflavone, Nimbinene, Nimbione, Nimbocinolide, Quercitrin, Vepnin, Saquinavir, and Nelfinavir were-7.32,-6.63,-6.69,-7.52,-5.27,-4.54,-6.07,-4.19,-5.02,-5.58,-6.23,-4.71, -3.72,-6.4,-7.14 and-4.67 kcal/mol respectively. The binding energies obtained from the docking of 6LU7 with the native ligand, Azadiradione, Nimbione, Vepnin, and Saquinavir were-6.14,-6.48,-6.79 and-6.49 kcal/mol correspondingly. The binding energies obtained from the docking of 2GTB with the native ligand, Azadiradione, Epiazadiradione, Epoxyazadiradione, Kaempferol, Meldenin, Myricetin, Nimbaflavone, Nimbione, Nimbocinolide, Quercitrin, Vepnin, Saquinavir, and Nelfinavir were-6.96,-7.13,-6.69,-5.22,-6.44,-5.06,-5.93,-6.66,-5.3,-5.63,-7.11,-6.89 and-5.42kcal/mol, respectively.

Conclusion: Azadiradione, Epiazadiradione, Nimbione, and Vepnin seemed to have the greatest potential to act as COVID-19 protease inhibitors. However, further research is necessary to explore their prospective medicinal use in vitro and in vivo conditions.

Keywords: COVID-19 Mpro, 6Y2E, 6LU7 Autodock, Azadirachta indica and Saquinavir


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1. Shivanshu S. Coronavirus (COVID-19): a pandemic disorder. Int J Pharm Pharm Res 2020;18:132-46.
2. Ahbanathul Missriya MA, Suhail Hassan. Assess the awareness and attitude regarding the prevention of Coronavirus disease in 2019. Asian J Pharm Clin Res 2020;13:95-8.
3. Wang C, Horby PW, Hayden FG, Gao GF. A novel coronavirus outbreak of global health concern. Lancet 2020;395:470-3.
4. Rohan RN, Rameshwar SC, Jaya PA, Sachin DS. The molecular docking study of potential drug candidates showing anti-covid-19 activity by exploring of therapeutic targets of SARS-CoV-2. EJMO 2020;4:185-95.
5. Wu C, Liu Y, Yang Y, Zhang P, Zhong W. Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharm Sin B 2020;10:766-88.
6. Ikita Pal, Shambaditya Goswami, Ravindra Pal Singh, Prashant Singh. A way to prevent the pandemic outbreak of nCOVID-19 in India. Asian J Pharm Clin Res 2020;13:39-40.
7. Bosch BJ, van der ZR, de Haan CA, Rottier PJ. The coronavirus spike protein is a class I virus fusion protein: structural and functional characterization of the fusion core complex. J Virol 2003;77:8801-11.
8. Siti K, Hendra K, Rizki A, Suhartati S, Soetjipto S. Potential inhibitor of covid-19 main protease (Mpro) from several medicinal plant compounds by molecular docking study. Preprints 2020;1-14. DOI:10.20944/preprints202003.0226.v1
9. Alzohairy MA. Therapeutics role of Azadirachta indica (Neem) and their active constituents in disease prevention and treatment. Evid Based Complement Alternat Med 2016;7382506.
10. Ahmad A, Javed MR, Rao AQ. Designing and screening of universal drug from neem (Azadirachta indica) and standard drug chemicals against influenza virus nucleoprotein. BMC Complement Altern Med 2016;16:519.
11. Christopher AL, Franco L, Beryl WD, Paul JF. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Delivery Rev 1997;23:3-25.
12. Gimenez B, Santos M, Marcio F, Fernandes J. Evaluation of blockbuster drugs under the Rule-of-five. Die Pharmazie 2010;65:148-52.
13. Chatterjee P, Nagi N, Agarwal A, Das B. The 2019 novel coronavirus disease (COVID-19) pandemic: a review of the current evidence. Indian J Med Res 2020;151:147-59.
14. Ramadan N, Shaib H. Middle East respiratory syndrome coronavirus (MERS-CoV): a review. Germs 2019;9:35-42.
15. Zhong NS, Zheng BJ, Li YM, Poon, Xie ZH, Chan KH, et al. Epidemiology and cause of severe acute respiratory syndrome (SARS) in Guangdong, People's Republic of China, in February 2003. Lancet 2003;362:1353-8.
16. Zhijian X, Cheng P, Yulong S, Zhengdan Z. Nelfinavir was predicted to be a potential inhibitor of 2019-nCov main protease by an integrative approach combining homology modelling, molecular docking and binding free energy calculation; 2020. p. 1201.
17. Shityakov S, Forster C. In silico predictive model to determine vector-mediated transport properties for the blood-brain barrier choline transporter. Adv Appl Bioinform Chem 2014;7:23.
18. Megha HS, Ram V, Uma SR. Molecular docking analysis of selected natural products from plants for inhibition of SARS-CoV-2 main protease. Curr Sci 2020;118:1087-92.
19. Kumar AHS. Molecular docking of natural compounds from tulsi (Ocimum sanctum) and neem (Azadirachta indica) against SARS-CoV-2 protein targets. BEMS Reports 2020;6:11-13.
20. Shanmuga SS. Some compounds from neem leaves extract exhibit binding affinity as high as-14.3 kcal/mol against COVID-19 main protease (Mpro): a molecular docking study, research square; 2020. p. 1-10.
21. Garba S, Mungadi HU. Quantitative chemical compositions of neem leaf aqueous extracts. Int J Res Sci Innov 2019;6:114-9.
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How to Cite
SHARON, S. F. B. “MOLECULAR DOCKING OF SELECTED BIOACTIVE COMPOUNDS FROM AZADIRACHTA INDICA FOR THE INHIBITION OF COVID19 PROTEASE”. International Journal of Pharmacy and Pharmaceutical Sciences, Vol. 12, no. 9, Sept. 2020, pp. 71-77, doi:10.22159/ijpps.2020v12i9.38875.
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